allele_freqs: Compute locus allele frequencies
In OchoaLab/simtrait: Simulate Complex Traits from Genotypes

Description Usage Arguments Value Examples

On a regular matrix, this is essentially a wrapper for colMeans or rowMeans depending on loci_on_cols. On a BEDMatrix object, the locus allele frequencies are computed keeping memory usage low.

1	allele_freqs(X, loci_on_cols = FALSE, mem_factor = 0.7, mem_lim = NA)

`X`	The genotype matrix (regular R matrix or BEDMatrix object). Missing values are ignored in averages.
`loci_on_cols`	If `TRUE`, X has loci on columns and individuals on rows; if false (the default), loci are on rows and individuals on columns. If X is a BEDMatrix object, columns are averaged to yield locus allele frequencies (regardless of the value of `loci_on_cols`).
`mem_factor`	BEDMatrix-specific, sets proportion of available memory to use loading genotypes. Ignored if `mem_lim` is not `NA`.
`mem_lim`	BEDMatrix-specific, sets total memory to use loading genotypes, in GB. If `NA` (default), a proportion `mem_factor` of the available memory will be used.

The vector of allele frequencies, one per locus. Names are set to the locus names, if present.

# Construct toy data
X <- matrix(
    c(0, 1, 2,
      1, 0, 1,
      1, NA, 2),
    nrow = 3,
    byrow = TRUE
)

# row means
allele_freqs(X)
c(1/2, 1/3, 3/4)

# col means
allele_freqs(X, loci_on_cols = TRUE)
c(1/3, 1/4, 5/6)